The proteolysis assistant can be invoked from the protein module. It can help with choosing proteases for limited proteolysis, separation of protein domains, etc. There are several list boxes which depend on each other, so it may appear confusing initially.

First and foremost, the protein is virtually cleaved by the proteases checked in the Proteases list. The cuts from all these proteases in the protein are shown in the Cuts list. The fragments resulting from these cuts are shown in the Resulting fragments list, as well as in the Gel simulation.

If you know that certain cuts do not take place (e.g., because the recognition motif is protected) you can deselect (uncheck) these cuts in the Cuts list.

If you know that certain annotated features of the protein are protected from proteases, you can check them in the Protect features list.

If you want to separate annotated features(e.g., domains) of your protein via proteases, you can select two or more features in the Separate fragments list. Depending on your selection and the state of Maximum number of proteases, the Cocktail suggestions list will be filled with proteases (or combinations of such) that will do the job. Selecting one of these "cocktails", a more detailed description will be shown below the list, and the respective proteases will be selected in the Proteases list.

The final result of all these settings is the Resulting fragments list. You can Sort fragments by cut position, fragment length, or size (weight). You can check individual fragments, All or None of them. Upon OK, several actions can be performed on the selected fragments:

Create selected fragments will create a new protein module for each selectged fragment

Annotate selected fragments will add a feature for each of the selected fragments in the current protein module

Keep proteases will add the proteases selected in the Proteases list to the current protein module